Within-species exploratory view · GSE43013

Horse native expression

Equus caballus

Sample QC, log-transformed PCA, and the most variable source-native feature IDs from Per-sample GEO-supplied FPKM files.

View PCA → Open Igf1 gene profile → Source samples → LACA content → Open GEO ↗
Samples
8
Native features
26,991
Expression unit
GEO-supplied FPKM
8 samples in this species view
26,991 source-native feature IDs
GSE43013 GEO-supplied FPKM
3 Table S1 tissues represented
Exploratory ordination

PCA of log1p native expression

SVD PCA after feature-wise centering after log1p(GEO-supplied FPKM). Axes apply only to this species and dataset.

Horse GSE43013 PCA Scatter plot of 8 samples. Each point is keyboard focusable and labelled by accession and tissue. eca.lv.1 · Liver · PC1 -92.08 · PC2 -49.78 eca.lv.2 · Liver · PC1 -89.61 · PC2 -47.52 eca.lv.3 · Liver · PC1 -88.55 · PC2 -43.10 eca.kd.1 · Kidney · PC1 4.30 · PC2 79.31 eca.kd.2 · Kidney · PC1 5.09 · PC2 82.81 eca.kd.3 · Kidney · PC1 3.72 · PC2 85.12 eca.br.1 · Brain · PC1 130.39 · PC2 -54.02 eca.br.2 · Brain · PC1 126.75 · PC2 -52.82
Observed ranges: PC1 -92.08 to 130.39; PC2 -54.02 to 85.12.

Tissue legend

  • Brain2
  • Kidney3
  • Liver3
Transform
log1p(GEO-supplied FPKM)
Feature policy
Intersection of native feature IDs across samples within each species.
Normalization
The source reports Cufflinks FPKM; LACA applies log1p only for within-species PCA/QC.
Sample-level quality context

Detected features and expression totals

These are descriptive summaries of the supplied GEO-supplied FPKM values—not read-depth QC metrics and not thresholds for sample exclusion.

Sample Tissue Detected native features Total GEO-supplied FPKM Median positive value
eca.lv.1 ↗ GSM1054999 Liver 17,746 4.151e+6 3.5878
eca.lv.2 ↗ GSM1055000 Liver 18,290 4.832e+6 3.5581
eca.lv.3 ↗ GSM1055001 Liver 17,085 4.089e+6 4.7299
eca.kd.1 ↗ GSM1055049 Kidney 18,170 8.303e+6 9.4712
eca.kd.2 ↗ GSM1055050 Kidney 18,619 4.900e+6 9.2275
eca.kd.3 ↗ GSM1055051 Kidney 18,531 5.877e+6 8.8191
eca.br.1 ↗ GSM1055094 Brain 19,743 4.660e+6 7.8431
eca.br.2 ↗ GSM1055095 Brain 19,228 5.208e+6 7.9346
Source-native feature ranking

Top variable native feature IDs

Ranked by variance after log1p transformation within this exact view. IDs are reported verbatim from the source matrix and must not be treated as cross-species orthologs.

  1. 01
    ENSECAG00000001248
    log1p variance
    26.3249
    mean native value
    10,201.6
    detected samples
    3/8
  2. 02
    tRNA-Ile
    log1p variance
    26.2579
    mean native value
    9,177.6
    detected samples
    4/8
  3. 03
    ENSECAG00000000964
    log1p variance
    25.8080
    mean native value
    77,154.0
    detected samples
    6/8
  4. 04
    ENSECAG00000013861
    log1p variance
    24.9777
    mean native value
    7,747.1
    detected samples
    5/8
  5. 05
    tRNA-Tyr
    log1p variance
    23.9263
    mean native value
    5,219.3
    detected samples
    4/8
  6. 06
    tRNA-Ala
    log1p variance
    21.5706
    mean native value
    20,008.4
    detected samples
    6/8
  7. 07
    ENSECAG00000008280
    log1p variance
    21.4084
    mean native value
    6,433.3
    detected samples
    8/8
  8. 08
    tRNA-His
    log1p variance
    21.3948
    mean native value
    4,857.6
    detected samples
    5/8
  9. 09
    ENSECAG00000025364
    log1p variance
    21.1532
    mean native value
    5,523.7
    detected samples
    2/8
  10. 10
    tRNA-Met
    log1p variance
    21.0178
    mean native value
    18,863.3
    detected samples
    6/8
  11. 11
    ENSECAG00000010083
    log1p variance
    21.0053
    mean native value
    3,872.4
    detected samples
    7/8
  12. 12
    ENSECAG00000026025
    log1p variance
    20.7213
    mean native value
    4,263.6
    detected samples
    5/8
  13. 13
    tRNA-Gly
    log1p variance
    20.6132
    mean native value
    2,450.0
    detected samples
    3/8
  14. 14
    tRNA-Leu-1
    log1p variance
    20.3488
    mean native value
    4,744.6
    detected samples
    5/8
  15. 15
    ENSECAG00000010239
    log1p variance
    20.1471
    mean native value
    6,186.2
    detected samples
    8/8
  16. 16
    ENSECAG00000014858
    log1p variance
    19.7514
    mean native value
    3,266.5
    detected samples
    7/8
  17. 17
    ENSECAG00000008365
    log1p variance
    19.2499
    mean native value
    4,822.0
    detected samples
    6/8
  18. 18
    ENSECAG00000025980
    log1p variance
    19.2123
    mean native value
    1,868.5
    detected samples
    3/8
  19. 19
    ENSECAG00000021580
    log1p variance
    19.1417
    mean native value
    18,484.9
    detected samples
    8/8
  20. 20
    ENSECAG00000027439
    log1p variance
    18.9995
    mean native value
    3,075.6
    detected samples
    2/8
  21. 21
    tRNA-Val
    log1p variance
    18.6982
    mean native value
    2,968.6
    detected samples
    2/8
  22. 22
    tRNA-Phe
    log1p variance
    18.3183
    mean native value
    2,604.3
    detected samples
    2/8
  23. 23
    ENSECAG00000025501
    log1p variance
    18.3145
    mean native value
    1,630.9
    detected samples
    3/8
  24. 24
    tRNA-Trp
    log1p variance
    18.2592
    mean native value
    1,457.7
    detected samples
    3/8
  25. 25
    ENSECAG00000022165
    log1p variance
    18.2248
    mean native value
    1,786.5
    detected samples
    6/8
Reproducible boundary

What this page computes—and what it does not

Input

Per-sample GEO-supplied FPKM files

The source reports Cufflinks FPKM; LACA applies log1p only for within-species PCA/QC.

Within-species computation

QC · PCA · variable features

Intersection of native feature IDs across samples within each species.

Not computed

No cross-species expression test

No matrix merge, differential-expression result, lifespan regression, or causal claim is presented here.

Source integrity

GSE43013_RAW.tar

SHA-256 550e7fd866249caa7d43d85beef62dd19f4d139cc41dae0b2d0a012ccb9e3bf1

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